Common Uses of PEAKS

Dan MaloneyBioinformatics Solutions Inc.

Insure Accurate Reporting

• Must understand what makes a good result– avoid false positives and negatives.

Agenda

• Walk through a PEAKS Search– Project creation– Search configuration– PEAKS DB results– de novo results

Project Creation

Add multiple samples

Select enzyme for each sample

Multiple Enzyme Approach

Multiple Enzyme Project

Glu C

Lys C

Trypsin

Multiple Enzyme Approach

Select ‘use enzyme specified in the sample’

PEAKS Complete Analysis

Launch everything from one screen

PEAKS Complete Analysis

Target + decoy database plotted

score

false

true

FDR#reported false hits

# reported hits

# of hits

An Idea to Improve Score Function

score

false

true

before after

Effect of similarity on scoring function

PEAKS DB Result

PEAKS DB Result

PTM Mutation

PEAKS DB Result

Set false discovery rate threshold

Pick a cut off

PEAKS DB Result

You may still have many hits below the threshold

PEAKS DB Result

PEAKS DB Result

Cannot actually count this protein

Confident PTMs and Mutations

de novo only view

Filtering de novo results

Only trust the highly confident amino acids

Filtering de novo results

Press this button to bring up the local confidence filter

Filtering de novo results

Set a local confidence cut off

Filtering de novo results

Amino acids below cut off will not be displayed, mass shown instead

De Novo Enabled PTM Discovery

good scan missed by protein ID

De Novo Enabled PTM Discovery

Was not found because dehydration was overlooked